Two years ago, when we moved to Davis, my wife and I kept talking about how absurdly friendly everyone was here. We still can't stop talking about it (yes, not everyone is friendly, but the average person is and I have never lived in a friendlier place).

Well, our feelings were confirmed by the recent Today show discussion of the five friendliest cities in the US and Davis was picked as one of them. Here is the video ...

Thursday, May 29, 2008

Yes that is right, Colbert is now obsessed with Microbes. He has started a new report ... "The Microbe Beat". On this first one, Colbert discusses Martian Microbes, Penicillin and other microbial things. This is perhaps the greatest coup for getting microbes the recognition they deserve since, well, since ever. Please make this the most watched Colbert video ever.

Wednesday, May 28, 2008

As I have said, I think Francis Collins, upon leaving the NHGRI, is well set up to become an advisor to some presidential candidate (not that I would pick him as my advisor if I were running, but alas I am not running this time around).

But if he does not become Obama's science sidekick or McCain's genomics guru, well, there are lots of things he might do. Here are some possibilities:

1. The 1000 genome songs project. He is already further along in this than the 1000 genomes project ...

2. Get a job at Craig Venter's Synthetic Genomics. Hey, Collins says he wants to try something new. And Craig has a history of hiring people who used to work at funding agencies.

Just got forwarded this email from Francis Collins to multiple people. Collins is stepping down. I wonder what specifically triggered this ... my guess is he is being recruited by one of the presidential candidates to be some sort of advisor. Nothing like having a prominent scientist who also is born again being on your team ....

Dear friends and colleagues in the many wonderful team projects that I have had the privilege of being part of,

I am writing to let you know of my plans to step down August 1, 2008 as Director of the National Human Genome Research Institute, a position that has been both a joy and privilege to hold for the past 15 years.

The key to success is having wonderful scientific opportunities and stellar colleagues with whom to work. Many challenges lie ahead as genomics increasingly becomes a leading force in medicine, and I leave my position supremely confident that NHGRI and NIH will continue to achieve notable success in meeting them.

Looking back, I'm tremendously proud of our collective work in leading the Human Genome Project (HGP) to its successful conclusion in 2003, and of our wide range of large-scale projects that built upon the foundation laid by the HGP. Collectively, these projects and the priceless data they generated have transformed biomedical research and empowered researchers all around the world. I'm also proud of these projects' commitments to protecting the privacy of genetic information and addressing the ethical, legal and social implications of genome research.

My decision to step down as NHGRI Director came only after much personal deliberation and was driven by a desire for an interval of time dedicated to writing, reflection and exploration of other professional opportunities in the public or private sectors. Rest assured that NHGRI's leadership will be in good hands. Alan E. Guttmacher, M.D., the current deputy director of NHGRI, will become acting director of NHGRI on August 1, and Mark Guyer, Ph.D., the long-time director of the Division of Extramural Research will continue his able leadership. A formal search process for a permanent NHGRI director will get underway shortly.

Finally, I'd like to let each of you know that while I may be leaving the NHGRI Director's office in search of other challenges, I will be cheering for the success of your dedicated and creative scientific achievements over the coming weeks, months, and years.

Ooh. Ahh. That is what we should all be saying as it has been announced that the first "female" genome has been sequenced. The press has eaten this up a bit, because of course, the other human genomes that have been sequenced have been from males.

Sure, in terms of public perception, it will be good to have a woman's genome sequenced. And in terms of science, there could be some major uses (e.g., if phenotypes such as health status are made available along with the genome one could try to use the genome to dissect female specific health issues). But as far as I can tell, this whole story is about perception with no reality involved.

The problem is that thethere is no there there yet. The data is not released. There is no paper (e.g., MSNBC reports ""No other scientists have yet verified the Dutch data, but some experts said they were eager to see the sequence.") This is just some group wanting to stake out some territory in an area that certainly others are working on at the same time. Their press release, by the way, has some icky stuff in it. Most annoying is that they make a point to emphasize that the woman whose genome was sequences is a clinical geneticist. And then they say

“If anyone could properly consider the ramifications of knowing his or her sequence, it is a clinical geneticist,” says professor Gert-Jan B van Ommen, leader of the LUMC team and director of the ‘Center for Medical Systems Biology’ (CMSB), a center of the Netherlands Genomics Initiative.

I do not even know what to say to this. What exactly makes a clinical geneticist better able to think about these issues than say, a genetic counselor, or a ethicist or a priest, or a bioinformatician?

Anyway, they also say

Following in-depth analysis, the sequence will be made public, except incidental privacy-sensitive findings

And for this, Lieden University is becoming the recipient of my second "Genomics By Press Release Award." (see my first one here, where interestingly, the discussion of sequencing a woman's genome came up when I announced I was going to sequence a genome on my new Excercycler machine).

Tuesday, May 27, 2008

Well, many people confuse me with my brother, Michael. I guess, if they do not know us, it is understandable. He is at Berkeley. I am at Davis. He works on genomics related things. So do I. We both are passionate about PLoS and Open Access publishing. We both went to Harvard. We both spent time at Stanford. I could go on (we used to look a bit alike ... see the lovely family portrait). Sure, sometimes I get sick of people asking me questions about microarray clustering software and Drosophila.

But most of the time, it only is good for me. Like today. If people want to confuse me with my brother today, fine by me. That is because today, HHMI announced the selection of their new "Investigators". Becoming an HHMI Investigator is the scientific equivalent of getting a sugar daddy. They give you money to do whatever research you want to do. They call it "People, not Projects." or something like that.

So - I saw some of the press on this and mostly it was very general - just talking about how HHMI is really important when NIH budgets are flat and all. But then this afternoon, I was listening to NPRs "Marketplace" when they do a story on the HHMI announcement. And I am thinking - wouldn't it be cool if they mention my brother? And so my ears perked up. And they discussed some background a bit and then Tom Cech, the head of HHMI, was explaining why they want to give money to people with no restrictions and he said

TOM CECH: Often in the course of research, you stumble upon leads to your question that were different from what you originally proposed and by funding the person, not the project, we are freeing people up to follow those leads.

For example, he says, one investigator started out studying retroviruses, but he switched gears and started building miniature arrays to look at the expression of genes in an organism -- don't worry, I have no idea what that means either.

CECH: But before long, he was looking at typing various sorts of leukemias and lymphomas and breast cancers. So he moved into the cancer area with tremendous results.

Certainly sounds like he was talking about my brother, who worked on flu viruses for part of his PhD (ok, they are not retroviruses, but they are RNA viruses), and did a post doc working on arrays (with Pat Brown and David Botstein) and also then used arrays to do cancer classification studies. Sure, he could also be talking about Pat Brown but hey, I am going to pretend he was talking about my brother since it is pretty close.

So, sure, I am a bit peeved they did not select me (thankfully, it seems on first glance that they people they did pick all pretty much rock in terms of science so it is not like I lost out to a bunch of dolts). But I am not jealous. Proud would be more accurate.

And it is time to place bets. Who out there thinks they will find some sort of evidence for life and how strong will that evidence be?

I for one think there will be life on Mars somewhere. And the Polar regions are not such a bad place to look for evidence of past or present life on the planet. Not sure what others out there think overall but here is some stuff from the web to consider:

Having witnessed two Mars lander failures, Mars Polar Lander before this blog was even born and Beagle-2 back when it was young and active (Landing and prelanding in the December 2003 archive, and the whole sad story in the Beagle-2 archive), and having been absent for all the other attempts that have proved successful, it seemed to me only prudent not to cover the landing of Phoenix this weekend

If you are interested in the funding of microbiology research from the National Science Foundation, there is a good opportunity coming up to find out what NSF's plans are and to give your input. James Collins, the Assistant Directory of the Biological Sciences Division at NSF will give a presentation at the ASM Meeting in Boston.

His presentation will be June 4, 2008

At the ASM Meeting at the Boston Convention and Exhibition Center

Room 052A

12-1:30 PM

If you are in town and interested in microbiology research funding, it would be worth going to give your input.

And if you are going to be in the area for the meeting or otherwise, you might consider going to the Division R Symposium that is from 8-10:30 in Room 156A. The talks in that session are:

Friday, May 23, 2008

When I left off in my notes the first day of the workshop was basically ending. After the session ended, the speakers and the members of the Institute of Medicine Forum on Microbial Threats went out to dinner at a restaurant in Cleveland Park. A few of us walked over to the Metro together and talked along the way. Thankfully, I did not get lost, as (1) I grew up in the DC area (2) I worked around the corner from where the workshop was held for a summer 20 years ago and (3) Julian Parkhill from the Sanger Center was with us and I had sadly gotten very disoriented with him when I was at a NIH Human Microbiome meeting in Bethesda which is actually where I grew up.

The dinner was quite good and I had some good conversations with various folks about microbes and their lives as well as about science in general. Sometimes these types of events are a bit much for me but for whatever reason the whole dinner event was very pleasant. And this was despite the fact that I still had not even started working on my talk for the next day. Finally, as some people were getting coffee Stanley Cohen and a few others said they wanted to head back to the hotel so a gaggle of us left, and went back.

I then spent a few hours making an outline of my talk and finding some slides and worrying about what I was going to say. I was going to be the last talk of the meeting -- in essence wrapping things up. Normally I do not get stressed about such things but here I was at this workshop in honor of one of the greatest biologists of the 20th century. And many scientist's I really really respect were to be in the audience. To give those who know an idea of how big a deal I thought this workshop was - I wore a suit for both days of the meeting. Now, I have not worn a suit in probably two years. But it just seemed natural to do it here. Anyway, with all of these things together it was a big deal to me to give the closing talk of the workshop.

And so I slept very little piecing together a talk that I hoped would honor Lederberg and make people glad they stayed until the end. On a side note, I never met Lederberg. But I was trained in microbiology by one of his students - Ann Ganesan who worked as a Senior Scientist in Phil Hanawalt's lab where I did my PhD. Ann was amazing -- the grand guru of microbiology and I learned a great deal from her. And thus I felt a connection to Lederberg even if I did not know him.

And finally, after very little sleep, I headed out for day 2 of the workshop. And day 2 was as good or better than day 1. There was Stanley Cohen talking about Lederberg and plasmids, Julian Davies (one of my all time favorite speakers) discussing antibiotic resistance, Jo Handelsman talking about functional metagenomics and microbial commensals in insects, Steven S. Morse talking about emerging diseases, Peter Daszak from the Consortium for Conservation Medicine, Mark Woolhouse talking about the ecology of human pathogens, and then me. All of the talks before me were quite excellent. Thoughtful. Insightful. Entertaining. (I do not think I have ever been at a meeting like this - I normally cannot sit through more than a few talks in a day). Lederberg would have been proud.

And then me. I think I did a good job with the wrap up. A lot of the talks for the day had been about how we can use an understanding of the past to help predict the future. And I talked about the original of novelty and how understanding how new functions originate can certainly help us understand the present (e.g., analyzing genome sequences) and I tried to bring in examples from all the other talks at the meeting (ahh .. one of those times where having my laptop and modifying my slides during the day was a good thing).

And then there was a brief discussion session where some really good questions/suggestions came up and then it was over. But I did come back inspired. Lederberg was such an incredible scientist and person. His legacy hopefully lives on.

Tuesday, May 20, 2008

A good short introduction by Peggy Hamburg of David Hamburg. Peggy is a scientist but had a funny story about how Lederberg gave her her first job - making cookies. She then introduced David Hamburg and said about him “he had many accomplishments including being my father”

Hamburg then gave a nice talk about Lederberg ... some highlights

When he was sick earlier this year, he still took time to come over to Hamburg's to discuss Hamburg's book that he was working on ... to give him input

Good story about Lederberg's building the department of genetics at Stanford

Told story about how Lederberg helped create the "human biology" major at Stanford

Emphasized that, despite the impression by many, Lederberg was not so aloof

Emphasized that Lederberg was deeply committed to educating the public about science and society and went to Hamburg one day saying he wanted Hamburg to introduce him to people at the Washington Post so he could write a column. And together they convinced the Post to do the column and Lederberg wrote it for many years. Many thought this was below someone with his scientific gifts but he was really committed to it. Note you can see his columns here See his papers here. I hope we would have liked blogging ...

Stephen Morse

Lederberg very interested in evolution

Coined phrase Exobiology

Good line of Lederberg's about how infectious disease is "our wits versus their genes and their have been evolving much longer"

Lederberg was an early adopter of email and bioinformatics and was a big fan of technology

In his office at Rockefeller, Lederberg had all sorts of awards posted in the outside office and then in his inner office he had two things on the wall. A picture of David Hamburg and his ham radio certificate.

Discussion

Peggy Hamburg said Lederberg used to take her tidepooling at Pescadero Beach

Lederberg seemed exceptionally fond of writing notes to people he knew to challenge them about some aspect of their work

Stanley Cohen mentioned how Lederberg was very helpful when he started out in the Genetics department at Stanford and when some people were questioning his desire to focus on plasmids

Julian Davies mentioned a story about giving his first "outside" talk - at Stanford - and being very nervous to go there with all the gurus of the field there. And Paul Berg warned him that Lederberg might appear to be sleeping during his talk but that he would ask some very challenging questions at the end. And Lederberg in fact did this - but that Julian had discussed the issue a bit during his talk. And with some trepidation, Julian said "Well, you may not have been listening ..." And though he was afraid of offending Lederberg, it did not.

Afternoon #1 - A really good session on beneficial microbes and microbial communities

Jill Banfield gave an exciting overview of her work on the Acid Mine Drainage ecosystem including examples of genome sequencing, proteomics, etc. But the most interesting part was a discussion of their work on microbe-virus interactions including looking at CRISPR elements. CRISPRs have been proposed (by Mojica et al, Makarova et al and some others) to be in essence a bacterial adaptive immune system to resist phage.

Jean-Michel Ane discussed plant-root symbioses including some very interesting stuff on how different symbionts interact with the same or overlapping host pathways.

Margaret McFall-Ngai discussed the Vibrio - Squid light organ symbiosis and among many things pointed out some detail about the signalling pathways and the develomental changes that occur in the squid

David Relman gave an overview of human microbiome studies and did a good job of pointing out not only what we know, but what we do not know.

Well, I am sitting in the Lederberg workshop right now with David Relman talking about Lederberg and the workshop. He is emphasizing how "microbes as threats" (which is similar to the name of the panel that convened this workshop) is a bit of a biased view point and that beneficial microbes are important too and that Lederberg recognized this. Relman is also mentioning the importance of Esther Lederberg (Josh Lederberg's first wife).

Now - some update on last night. I got to the hotel around 3 went walking around DC and then came back to the hotel. All the speakers were supposed to be staying there so I lingered in the lobby hoping to bump into people I knew and find someone to go to dinner with. And I sat down and started reading a book I just got - Microcosm by Carl Zimmer. Zimmer's book is about E. coli and the history of studies of this magnificent organisms. And I started by lookng up in the index the stuff on Lederberg and read that. The book really seems to be quite excellent --- it covers a wide range of topics in biology at the same time as highlighting the importance of this organism. And then the gurus of microbiology started coming by. And I snookered my way into dinner with Julian Davies, Bruce Levin and Stanley Cohen. And it ewas a great time --- talking about Lederberg, microbes, plasmids, selection, etc. A good start to the meeting for me. More later.

By papers they mean everything - letters, notes, drafts, communications, etc. It is quite comprehensive and quite interesting including many discussions with other leading researchers key moments in the history of 20th century biological sciences research. It is worth checking out. I note - despite the availability of this great collection, one part of this life as a scientists is not completely freely available - his publications. Not all are at this site and many are hidden behind the walls of various journals. What a shame. Just about every one of his papers is worth reading.

The workshop is put on by the Institute of Medicine in Washington DC and it is open to the public. You have to register in advance and I am not sure how many more slots are available but it looks to be pretty good. The sessions topics are are: "The microbiome and co-evolution" "Microbial evolution and the emergence of virulence" "Mechanisms of resistance" "Anticipation of future emerging infectious diseases" and there are some heavy hitter speakers in there including David Relman, Jo Handelsman, Jill Banfield, Margaret Mcfall-Ngai, Stanley Falkow, Bruce Levin, Julian Parkhill, Stanley Cohen, Julian Davies, Steven Morse, Ian Lipkin, and well, me.

I will be blogging from there, but if you are in the DC area or can be, it could be a good workshop.

I am also going to be writing a bit more about Lederberg and his favorite bug (E. coli) in the next few days so stay tuned ...

In my continuing series on Open Evolution I am posting an email I got regarding the creation of a new mailing list on "Open Taxonomy". For more on Open Taxonomy see "The Other 95%" which has some really good stuff on it.

Under the umbrella of the Open Biomedical Ontologies project (OBO; http://obofoundry.org/) we have created a new mailing list, called obo-taxonomy, for the discussion of ontological representation of taxonomies and phylogenies. The OBO Foundry supports the development of orthogonal, interoperable reference ontologies for biological science.

The Phenoscape project (http://phenoscape.org) develops methods and tools for using ontologies to integrate comparative morphological data with mutant phenotypes of genetic model organisms. As such we are very interested in participation from members of the evolutionary biology community to explore how best to integrate taxonomy into an ontological framework. Issues include proper semantics of the relationship between taxonomic groups, and between specimens and species.

Subscribe to the mailing list:https://lists.sourceforge.net/lists/listinfo/obo-taxonomy

Tuesday, May 13, 2008

Well, much as I hate to admit it, I find myself agreeing with the notion that cuteness sells in genome sequencing. That is in essence the claim of Natalie Anger in an article in the New York Times about all the attention the platypus genome paper has been receiving over the last week (seeA Gene Map for the Cute Side of the Family - New York Times

Alas, microbiologists really do not have anything like this no? I mean, who feels that E. coli or yeast are, well, cute? (Well, even if you have one of those "giant microbes" stuffed animals, that just means you are a dork like me ... the public does not collect those). Sure, Carl Zimmer can get some attention for all the geeky tattoos out there and some of them did have something to do with microbes, but again, a platypus they are not.

So what are we forlorn microbiologists to do? We need better PR and imagery. We need cute microbes. We need more dark and evil microbes too (I mean, if anyone sequenced the T-rex genome - for real - it would get attention too).

So - I am calling all microbiologists and microbiology fans --- bring forth your imagery that will help microbes get the attention they deserve. And today I am suggesting just one simple thing we can all do to make a difference: get some new names.

That is, give your favorite microbe a good common name or nickname to bring out the cuddly or dark imagery we need. All microbes names should conjure up something to the public, like anthrax does (yes, I know, anthrax is the disease and not the microbe , but this adherence to rules is part of the problem we have).

Wednesday, May 07, 2008

All I can say is I am glad I check my medicines before I take them. I went to Long's in East Davis the other day to pick up some insulin and was given a box of my insulin pens. When I got home I found that there was only one insulin pen in the box and that pen was used. Not exactly confidence boosting in my pharmacy. Only later did I figure out what happened which was even scarier. This was insulin I had returned months before because of a defect that Long's was supposed to send back to the manufacturer (I had called the company who had handled this very well, and they told me a free box would be at Long's and that Long's would return the unused portion to them). So I guess Long's put it in the fridge and did not return it and then saw my name on it and gave it back to me. Yuck. Even worse, they did it again, I think the next time I went in. Double yuck.

Note that I wrote this when it happened but decided not to post it (but saved it in my blogger account), since it seemed a bit too personal. But now (2009) I am having problems with Long's again and I figured I would make live some of my old postings about Long's.

In the guide they have an overview of the new Harvard Open Access policy, suggestions for what one can do on one's own campus and a plan of action for bringing about policy change. I know I am going try some of their suggestions here at Davis as I am hoping Davis and the UC in general adopts a policy like Harvard's (they mention the UC consideration of such a policy in their site)

Thursday, May 01, 2008

Good Open Access news from Rockefeller Press. They have decided to change their publishing policies and are making them much more open. Emma Hill, who used to work at PLoS Biology and is now the Editor of J. Cell Biol. from Rockefeller has an editorial (with Mike Rossner) about the change including details of the new policy and some of the reasons for the change.

Among the changes they make and some of the reasons why

Giving copyright to the authors.

This is a good thing and about time for them to do it. They say: "Preying on authors' desire to publish, and thus their willingness to sign virtually any form placed in front of them, scientific publishers have traditionally required authors to sign over the copyright to their work before publication. "

Adopting a Creative Commons license.

They say "What does this Creative Commons License mean? It means that our published content will be open for reuse, distribution, data mining, etc., by anyone, as long as attribution is made to the original work. Share-alike means that any subsequent distribution must follow the rules set out in this license. Non-commercial means that published work can be reused without permission, as long as it is for noncommercial purposes."

This to me is the most important part of their policy. CC licenses change everything - they make it easy for everyone to use the material.

They retain an exclusive license for 6 months. After the 6 months, the material has the full CC license and can be distributed anywhere as long as it is attributed and not for commercial use.

Overall, I think this change is a good thing. It is still not the full Open Access I prefer, but it is a great step in the right direction. Also see a blog by Science Commons discussing the new policy - see Science Commons. They are overwhelmingly positive. See also Peter Suber here.

On extra nice thing about the policy is they are making it retroactive for all their publications in the past. So lots of Rockefeller press stuff from the past has now become much more open.

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Some disclosures that might be relevant to what I write about:1. I am involved with the Public Library of Science in multiple ways, and my brother was a co-founder. I receive no money from them (although in theory I can get compensated for expenses).2. My wife worked for Mendel Biotechnology many years ago and we still own a small amount of their stock.3. I make some money from sales of my Evolution textbook.

4. I am on the Scientific Advisory Board of uBiome and Symbiota for which I get some stock options.

5. I have received some research funding from the MARS Corporation (for work on dog microbiomes and plant microbiomes).